Hi, thank you very much for the useful tool.
After running circr for three days, I found that the script has no output and no errors（This script runs on a HPC with enough disk space and memory）. It seems that the script is suspended at the filter_interactions step. Can you give me more useful information?
Here is the log of the script running:
09/16/2022 11:37:28 AM - INFO: Running analysis on /soft_test/CIRCexplorer2/ciri/ciri.output.gtf.bed; genome set to human and version hg19
09/16/2022 11:37:28 AM - INFO: Retrieving exon information
09/16/2022 11:37:28 AM - INFO: Loading input bed file: /soft_test/CIRCexplorer2/ciri/ciri.output.gtf.bed
09/16/2022 11:37:28 AM - INFO: Loading input GTF file: /soft_test/circdb/Circr-main/Circr/support_files/human/hg19/hg19.ensGene.gtf
09/16/2022 11:37:28 AM - INFO: Loading rRNA file: /soft_test/circdb/Circr-main/Circr/support_files/human/hg19/hg19.rRNA.bed
09/16/2022 11:37:30 AM - INFO: Generating exons dataframe and polishing data
09/16/2022 11:37:30 AM - INFO: Returning dataframe
09/16/2022 11:37:30 AM - INFO: Creating Circular Database and Retrieving Coordinates
09/16/2022 11:37:30 AM - INFO: Calculating circulars coordinates
09/16/2022 11:37:40 AM - INFO: Retrieving FASTA sequences
09/16/2022 11:37:40 AM - INFO: Performing analysis with RNAhybrid, miRanda and TargetScan
09/16/2022 11:37:40 AM - INFO: Setting the processes for the three software run up
09/16/2022 11:37:43 AM - INFO: Running miRNA:circRNA binding site predictions
09/16/2022 01:57:39 PM - INFO: Parsing RNAhybrid's output files
09/16/2022 03:20:07 PM - INFO: Collecting results into a single location
09/17/2022 11:36:07 PM - INFO: Returning collected data
09/17/2022 11:36:07 PM - INFO: Merging overlapping seed predictions
09/17/2022 11:42:10 PM - INFO: Adding Annotation to Predicted Interactions
Here is the command of the script running:
Circr.py -i ciri.output.gtf.bed -s human -v hg19 -o example_circr.csv
Hi, thank you very much for the useful tool. After running circr for three days, I found that the script has no output and no errors（This script runs on a HPC with enough disk space and memory）. It seems that the script is suspended at the filter_interactions step. Can you give me more useful information? Here is the log of the script running:
09/16/2022 11:37:28 AM - INFO: Running analysis on /soft_test/CIRCexplorer2/ciri/ciri.output.gtf.bed; genome set to human and version hg19 09/16/2022 11:37:28 AM - INFO: Retrieving exon information 09/16/2022 11:37:28 AM - INFO: Loading input bed file: /soft_test/CIRCexplorer2/ciri/ciri.output.gtf.bed 09/16/2022 11:37:28 AM - INFO: Loading input GTF file: /soft_test/circdb/Circr-main/Circr/support_files/human/hg19/hg19.ensGene.gtf 09/16/2022 11:37:28 AM - INFO: Loading rRNA file: /soft_test/circdb/Circr-main/Circr/support_files/human/hg19/hg19.rRNA.bed 09/16/2022 11:37:30 AM - INFO: Generating exons dataframe and polishing data 09/16/2022 11:37:30 AM - INFO: Returning dataframe 09/16/2022 11:37:30 AM - INFO: Creating Circular Database and Retrieving Coordinates 09/16/2022 11:37:30 AM - INFO: Calculating circulars coordinates 09/16/2022 11:37:40 AM - INFO: Retrieving FASTA sequences 09/16/2022 11:37:40 AM - INFO: Performing analysis with RNAhybrid, miRanda and TargetScan 09/16/2022 11:37:40 AM - INFO: Setting the processes for the three software run up 09/16/2022 11:37:43 AM - INFO: Running miRNA:circRNA binding site predictions 09/16/2022 01:57:39 PM - INFO: Parsing RNAhybrid's output files 09/16/2022 03:20:07 PM - INFO: Collecting results into a single location 09/17/2022 11:36:07 PM - INFO: Returning collected data 09/17/2022 11:36:07 PM - INFO: Merging overlapping seed predictions 09/17/2022 11:42:10 PM - INFO: Adding Annotation to Predicted Interactions
Here is the command of the script running: Circr.py -i ciri.output.gtf.bed -s human -v hg19 -o example_circr.csv